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- PDB-5n2a: METHYL-COENZYME M REDUCTASE III FROM METHANOTORRIS FORMICICUS TRI... -

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Basic information

Entry
Database: PDB / ID: 5n2a
TitleMETHYL-COENZYME M REDUCTASE III FROM METHANOTORRIS FORMICICUS TRIGONAL FORM
Components
  • (Methyl-coenzyme M reductase, ...Coenzyme-B sulfoethylthiotransferase) x 2
  • Methyl-coenzyme M reductase subunit alphaCoenzyme-B sulfoethylthiotransferase
KeywordsTRANSFERASE / POST-TRANSLATIONAL MODIFICATION / BINDING SITES / CATALYSIS / COENZYMES / DISULFIDES / HYDROGEN / HYDROGEN BONDING / LIGANDS / MESNA / METALLOPORPHYRINS / METHANE / METHANOCOCCALES / NICKEL / OXIDATION-REDUCTION / OXIDOREDUCTASES / PHOSPHOTHREONINE / PROTEIN CONFORMATION / PROTEIN FOLDING / PROTEIN STRUCTURE / THERMOPHILE / AUTOTROPH / HYDROXY-TRYPTOPHANE
Function / homology
Function and homology information


coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / metal ion binding
Similarity search - Function
Methyl-coenzyme M Reductase; Chain B, domain 2 / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Alpha-Beta Plaits - #470 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit ...Methyl-coenzyme M Reductase; Chain B, domain 2 / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Alpha-Beta Plaits - #470 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal / Methyl-coenzyme M reductase, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit / Methyl-coenzyme M reductase beta subunit, C-terminal domain / Methyl-coenzyme M reductase beta subunit, N-terminal domain / Methyl-coenzyme M reductase, alpha subunit, N-terminal / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Methyl-coenzyme M reductase, ferredoxin-like fold / Methyl-coenzyme M reductase, alpha subunit, C-terminal / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 2 / Methyl-coenzyme M reductase alpha subunit, C-terminal domain / Methyl-coenzyme M reductase alpha subunit, N-terminal domain / Lambda Exonuclease; Chain A / Alpha-Beta Plaits / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / 1-THIOETHANESULFONIC ACID / FACTOR 430 / : / Coenzyme B / Methyl-coenzyme M reductase subunit alpha / Methyl-coenzyme M reductase subunit gamma / Methyl-coenzyme M reductase subunit beta
Similarity search - Component
Biological speciesMethanotorris formicicus Mc-S-70 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWagner, T. / Wegner, C.E. / Ermler, U. / Shima, S.
CitationJournal: J.Bacteriol. / Year: 2017
Title: Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales.
Authors: Wagner, T. / Wegner, C.E. / Kahnt, J. / Ermler, U. / Shima, S.
History
DepositionFeb 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 2.0Apr 24, 2019Group: Atomic model / Data collection / Database references / Category: atom_site / citation / pdbx_database_proc
Item: _atom_site.occupancy / _citation.journal_abbrev ..._atom_site.occupancy / _citation.journal_abbrev / _citation.journal_volume / _citation.title
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-coenzyme M reductase subunit alpha
B: Methyl-coenzyme M reductase, beta subunit
C: Methyl-coenzyme M reductase, gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,5088
Polymers138,9973
Non-polymers1,5115
Water0
1
A: Methyl-coenzyme M reductase subunit alpha
B: Methyl-coenzyme M reductase, beta subunit
C: Methyl-coenzyme M reductase, gamma subunit
hetero molecules

A: Methyl-coenzyme M reductase subunit alpha
B: Methyl-coenzyme M reductase, beta subunit
C: Methyl-coenzyme M reductase, gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,01616
Polymers277,9946
Non-polymers3,02210
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area55190 Å2
ΔGint-289 kcal/mol
Surface area61970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.699, 127.699, 160.376
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-604-

K

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methyl-coenzyme M reductase subunit alpha / Coenzyme-B sulfoethylthiotransferase


Mass: 61180.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: IN CHAIN A, RESIDUE 260 IS A N1-METHYLHISTIDINE. RESIDUE 274 IS A C5-(S)-METHYLARGININE. RESIDUE 402 IS A C2-(S)-METHYLGLUTAMINE. RESIDUE 429 IS A POSSIBLE 6-HYDROXY-TRYPTOPHANE. RESIDUE 447 IS A THIOGLYCINE.
Source: (natural) Methanotorris formicicus Mc-S-70 (archaea)
Cell line: / / Organ: / / Plasmid details: DSMZ / Variant: Wild-type / Tissue: /
References: UniProt: H1KXL5, coenzyme-B sulfoethylthiotransferase

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Methyl-coenzyme M reductase, ... , 2 types, 2 molecules BC

#2: Protein Methyl-coenzyme M reductase, beta subunit / Coenzyme-B sulfoethylthiotransferase


Mass: 47541.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanotorris formicicus Mc-S-70 (archaea)
Cell line: / / Organ: / / Plasmid details: DSMZ / Variant: Wild-type / Tissue: /
References: UniProt: H1KXL9, coenzyme-B sulfoethylthiotransferase
#3: Protein Methyl-coenzyme M reductase, gamma subunit / Coenzyme-B sulfoethylthiotransferase


Mass: 30274.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanotorris formicicus Mc-S-70 (archaea)
Cell line: / / Organ: / / Plasmid details: DSMZ / Variant: Wild-type / Tissue: /
References: UniProt: H1KXL6, coenzyme-B sulfoethylthiotransferase

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Non-polymers , 5 types, 5 molecules

#4: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O3S2
#5: Chemical ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE / Coenzyme B


Mass: 343.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22NO7PS
#6: Chemical ChemComp-F43 / FACTOR 430 / Cofactor F430


Mass: 906.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H51N6NiO13
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.34 % / Description: Yellow cubic crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Three single crystals appeared after one year and could be immediately fished. The drop contained a mixture of 0.8 ul of 35 mg/ml of MCR III Methanotorris formicicus and 0.8 ul of the ...Details: Three single crystals appeared after one year and could be immediately fished. The drop contained a mixture of 0.8 ul of 35 mg/ml of MCR III Methanotorris formicicus and 0.8 ul of the reservoir solution containing 200 mM potassium bromide, 200 mM potassium thiocyanate, 100 mM Na cacodylate pH 6.5, 3% (w/v) PGA-LM, and 30% PEG 400 (v/v).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.8→48.13 Å / Num. obs: 37773 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 62.56 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.094 / Net I/σ(I): 7.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5454 / CC1/2: 0.334 / Rpim(I) all: 0.371 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.0.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A8W

5a8w


Resolution: 2.8→39.85 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.8968 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.306
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 1898 5.03 %RANDOM
Rwork0.198 ---
obs0.1991 37735 99.88 %-
Displacement parametersBiso mean: 61.19 Å2
Baniso -1Baniso -2Baniso -3
1-3.1879 Å20 Å20 Å2
2--3.1879 Å20 Å2
3----6.3758 Å2
Refine analyzeLuzzati coordinate error obs: 0.369 Å
Refinement stepCycle: 1 / Resolution: 2.8→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9662 0 92 0 9754
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00810019HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0113597HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3500SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes254HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1468HARMONIC5
X-RAY DIFFRACTIONt_it10019HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.55
X-RAY DIFFRACTIONt_other_torsion18.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1295SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11999SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2537 142 4.87 %
Rwork0.2444 2772 -
all0.2448 2914 -
obs--99.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0711-0.09920.11790.8277-0.33520.1749-0.11560.03030.09240.02110.1554-0.0778-0.08120.0814-0.0399-0.0381-0.043-0.0244-0.01370.0224-0.0345-24.42516.975322.5389
20.05540.18030.20110.4218-0.13070.4823-0.06470.0208-0.0022-0.03630.03520.02560.01710.00250.0296-0.0193-0.08580.0129-0.13860.06350.0843-58.5839-0.11179.3743
30.3883-0.0239-0.3589-0.1570.321.1568-0.03970.0745-0.0606-0.0309-0.0088-0.0026-0.02460.00080.04850.1026-0.10870.04-0.1229-0.0087-0.0209-37.345713.7317-14.7026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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